I have a dual boot system. My bios lets me choose which hard drive I want to boot from. My largest drive 120g is my NTFS partition. It is an eide drive and is configuared for cable select. I have that divided into XP partition(windows os) and a second partition to store documents and music etc in case XP crashes and needs reinstalled(so far I have never had to yet even after 2years). So That is drives C:\ and E:\ in NTFS. My second hard drive is smaller 20g and was from my old computer. That is in Fat32 and has my Win98 os on it. I use that one for games and other older applications that cannot play nice with XP

. Especially dos games. That drive also has the jumper settings placed for cable select, and is on the same ide cable. I placed them on the cable for the master/slave configuration (XP master and 98 slave. That way if XP will boot up by default if I don't choose something.
NTFS is very stable with XP. I can see both drives with NTFS and Xp. That way I can back up documents etc to that drive as an extra backup.
When I boot to Win98, (Using my bios and selecting that hard drive to boot to)it only sees that drive that has the Win 98 os.
NTFS is the most stable, if you completely change the drive to NTFS format then install XP.
I hope that gives you info. Oh...The other piece of info is that NTFS works best on Hard drives that are bigger than 80g. If yours is smaller, than I would not change it. You would not see any benefit from it.